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The H-factor as a novel quality metric for homology modeling

Eric di Luccio12* and Patrice Koehl1

Author Affiliations

1 Computer Science Department, University of California Davis, 451 East Health Sciences Drive, Room 4337, Genome Center, GBSF, Davis, CA, 95616, USA

2 School of Applied Biosciences, Kyungpook National University, Agriculture and life science building #3, room 309, 1370 Sangyeok-dong, Buk-gu, Daegu, 702-701, Republic of Korea

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Journal of Clinical Bioinformatics 2012, 2:18  doi:10.1186/2043-9113-2-18

Published: 2 November 2012



Drug discovery typically starts with the identification of a potential target that is then tested and validated either through high-throughput screening against a library of drug compounds or by rational drug design. When the putative target is a protein, the latter approach requires the knowledge of its structure. Finding the structure of a protein is however a difficult task. Significant progress has come from high-resolution techniques such as X-ray crystallography and NMR; there are many proteins however whose structure have not yet been solved. Computational techniques for structure prediction are viable alternatives to experimental techniques for these cases. However, the proper validation of the structural models they generate remains an issue.


In this report, we focus on homology modeling techniques and introduce the H-factor, a new indicator for assessing the quality of protein structure models generated with these techniques. The H-factor is meant to mimic the R-factor used in X-ray crystallography. The method for computing the H-factor is fully described with a demonstration of its effectiveness on a test set of target proteins.


We have developed a web service for computing the H-factor for models of a protein structure. This service is freely accessible at webcite.